Coarse grain simulation of Bio-molecular patchy spherocylinders

Abstract

This project aims at simulating aggregates of Amyloid-Beta (Aβ) peptides, which are characteristic of Alzheimer’s disease. These peptides aggregate to form long chained fibrils that are characterised by the progression of the Alzheimer’s disease. We apply a model developed by Sari´c et al. (2014 and 2016) which ˇ uses Coarse Grain Monte Carlo simulations of Spherocylinders with Patches that mimic non-specific interactions, these structures represent the peptide Amyloid-Beta (Aβ) molecules. For the simulation, we have created our own Simulation framework in C++ from ground up. Thus a great focus have been given to working on various algorithms, figures of merit, and testing of the components of the simulation. We have tried to obtain some results reported in the literature to test the modifications we have done on the model and also find the nature of interactions and the system state for some novel structures that were obtained by one of our collaborators. The basis of the model has been to reduce bio-chemical complexity and incorporate it into the physical complexity of the problem. Thus, inferences about different environments can be produced by just considering the physical boundaries of the system state